The government said the decision to close the much-criticised facility was "another milestone in the ramping-down of Australia's onshore immigration detention network."
Maribyrnong opened in the middle of the last century, but has recently been the site of hunger strikes and other protests over harsh treatment.
In 2017, the Australian Human Rights Commission - a government body - reported guards at the facility used "more restrictive measures than necessary," including the excessive use of restraints during escort.
The few remaining inmates have now been transferred to other facilities.
Immigration Minister David Coleman said successful policies had reduced the number of people held at Australia's immigration detention centres from a peak of 10,000 in 2013 to just over a thousand today.